feat: bump to dna-seq-benchmark 1.12.2 (#49)

Co-authored-by: Bianca Stöcker <[email protected]>
Co-authored-by: Johannes Köster <[email protected]>
Co-authored-by: Johannes Koester <[email protected]>

Author: 3 people

.github/workflows/main.yml

@@ -34,12 +34,12 @@ jobs:
           echo "current branch: ${{ github.ref }}"
 
       - name: Free Disk Space (Ubuntu)
-        uses: jlumbroso/[email protected].0
+        uses: jlumbroso/[email protected].1
         with:
           # this might remove tools that are actually needed,
           # if set to "true" but frees about 6 GB
           tool-cache: false
-          
+
           # all of these default to true, but feel free to set to
           # "false" if necessary for your workflow
           android: true
@@ -48,63 +48,68 @@ jobs:
           large-packages: true
           swap-storage: true
           docker-images: false
-          
+
       - name: Check out repository code
         uses: actions/checkout@v2
 
       - name: Download reference genome
-        uses: snakemake/snakemake-github-action@v1
+        uses: snakemake/snakemake-github-action@v2
         with:
           directory: "."
           snakefile: "workflow/Snakefile"
-          args: "--cores 1 --use-conda --conda-cleanup-pkgs cache resources/reference/genome.fasta"
+          args: "--cores 1 --sdm conda --conda-cleanup-pkgs cache resources/reference/genome.fasta"
           stagein: |
-            pip install snakemake-storage-plugin-zenodo snakemake-storage-plugin-http
+            pip install snakemake-storage-plugin-zenodo 
+            pip install snakemake-storage-plugin-http
 
       - name: Download truthsets
-        uses: snakemake/snakemake-github-action@v1
+        uses: snakemake/snakemake-github-action@v2
         with:
           directory: "."
           snakefile: "workflow/Snakefile"
-          args: "--use-conda --cores 1 --conda-cleanup-pkgs cache --until benchmark_get_truth"
+          args: "--sdm conda --cores 1 --conda-cleanup-pkgs cache --until benchmark_get_truth"
           stagein: |
-            pip install snakemake-storage-plugin-zenodo snakemake-storage-plugin-http
+            pip install snakemake-storage-plugin-zenodo 
+            pip install snakemake-storage-plugin-http
 
       # This step is necessary (after downloading the truthsets above) to ensure
       # that the files coming from the git repo are not triggering reruns
       # because their modification dates are too new or too old.
       # (as git does not preserve modification dates)
       - name: Fix modification dates
-        uses: snakemake/snakemake-github-action@v1
+        uses: snakemake/snakemake-github-action@v2
         with:
           directory: "."
           snakefile: "workflow/Snakefile"
-          args: "--cores 1 --touch resources/regions/*/test-regions.cov-*.bed"
+          args: "--cores 1 --sdm conda --touch resources/regions/*/test-regions.cov-*.bed"
           stagein: |
-            pip install snakemake-storage-plugin-zenodo snakemake-storage-plugin-http
+            pip install snakemake-storage-plugin-zenodo 
+            pip install snakemake-storage-plugin-http
 
       - name: Run analysis
-        uses: snakemake/snakemake-github-action@v1
+        uses: snakemake/snakemake-github-action@v2
         with:
           directory: "."
           snakefile: "workflow/Snakefile"
           args: >
-            --cores 2 --use-conda --conda-cleanup-pkgs cache
+            --cores 2 --sdm conda --conda-cleanup-pkgs cache --rerun-triggers mtime --all-temp
           stagein: |
-            pip install snakemake-storage-plugin-zenodo snakemake-storage-plugin-http
+            pip install snakemake-storage-plugin-zenodo 
+            pip install snakemake-storage-plugin-http
 
       - name: Create report
-        uses: snakemake/snakemake-github-action@v1
+        uses: snakemake/snakemake-github-action@v2
         with:
           directory: "."
           snakefile: "workflow/Snakefile"
           args: "--report report.zip"
           stagein: |
-            pip install snakemake-storage-plugin-zenodo snakemake-storage-plugin-http
+            pip install snakemake-storage-plugin-zenodo 
+            pip install snakemake-storage-plugin-http
 
       - name: Upload report as artifact
 
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: report
           path: report.zip